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2,556 results for “assemblages”
Data from: Linking divergence in phenotypic selection on floral traits to divergence in local pollinator assemblages in a pollination-generalized plant
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Functional and phylogenetic structure of forest bird assemblages along an Afrotropical elevational gradient
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Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region
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Impact of the 2011 Tohoku earthquake on the species diversity of rocky intertidal sessile assemblages
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Data from: Human presence and infrastructure impact wildlife nocturnality differently across an assemblage of mammalian species
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Beneficial insect assemblages in floral strips and comparison fields
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Cheilostome cyclostome assemblage 2020
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Data to support manuscript: A Comparison of Two ROV Survey Methods Used to Estimate Fish Assemblages and Densities Around a California Oil Platform
This fish dataset was collected at platform Harmony, between Aug 25 and Aug 26, 2018. The ROV fish survey was done with two methods: industry (mimicking an inspection survey conducted for platform structural inspections) and biological method. Due to differences between the two methods in the positioning of the ROV vis a vis the jacket crossbeams, fish densities and diversities were different between the two methods at the platform bottom. This dataset provides fish counts and the relevant survey parameters (transect length and depth).
Microhabitat use in a stream fish assemblage
We quantified microhabitat use by members of a southern Appalachian stream fish assemblage over a ten-year period that included both floods and droughts. Our study site (37 m in length) encompassed riffle, run and pool habitats. Previous research indicated that species belonged to either benthic or water-column microhabitat guilds. We examined microhabitat use among fishes in a 37 m section of Coweeta Creek, NC., over a ten-year period (1983-1992) that included both floods and droughts. Multivariate comparison using Principal Component analysis of fish use data was contrasted with habitat availability.
Stream fish assemblage stability in a southern Appalachian stream at the Coweeta Hydrologic Laboratory from 1984 to 1995
Stream fish abundance data was collected seasonally in three 30m sections of stream from 1984 to 1995. Population estimates were obtained using electrofishing (3 pass removal). Habitat availability measurements were recorded biannually along with the electrofishing data starting in fall 1988. Data was collected each fall and spring from 1988-1995, in order to examine changes in fish assemblage structure along the habitat gradient. We used strong inference with Akaike’s Information Criterion (AIC) to assess the processes capable of explaining long-term (1984–1995) variation in the per capita rate of change of mottled sculpin (Cottus bairdi) populations in the Coweeta Creek drainage (USA). We sampled two fourth- and one fifth-order sites (BCA [uppermost], BCB, and CC [lowermost]) along a downstream gradient, and the study encompassed extensive flow variation.
Reintroduced grazers and prescribed fire effects on beetle assemblage structure and function in restored grasslands
<p>Ecological restoration seeks to re-establish functioning ecosystems, but planning and evaluation often focus on taxonomic community structure and neglect consumers and their functional roles. The functional trait composition of insect assemblages, which make up the majority of animal diversity in many systems, can reveal how they are affected by restoration management and the consequences for ecosystem function. We sampled ground beetle (Coleoptera: Carabidae) assemblages in restored tallgrass prairies varying in management with prescribed fire and reintroduced American bison (<i>Bison bison</i>) to describe their taxonomic and functional trait structure. We also measured seed and arthropod predation to relate management, beetle assemblage characteristics, and function, and to test if function is maximized by trait diversity, dominant trait values, or beetle abundance. Beetle assemblages primarily varied with restoration age, declining over time in richness and both taxonomic and functional diversity, but bison presence also influenced taxonomic composition. Prescribed fire reduced seed predation in summer and arthropod predation in fall. Although seed predation was unrelated to beetle assemblages, arthropod predation was greater in sites with higher abundances of carnivorous ground beetles. The relatively weak impacts of fire and bison on functional assemblage structure is a promising sign that these management disturbances, aimed at supporting a diverse native plant community, are not detrimental to beetle assemblages. The significance of reduced predator function following prescribed fire will depend on the restoration context and whether seed or arthropod predation relates to management goals.</p>
Figure 1 in Patterns of spatial variability of mobile macro-invertebrate assemblages within a Posidonia oceanica meadow
Figure 1. Map of Pianosa Island. Stars indicate the study areas.
The community structure of bird assemblages on urban Strangler figs
Figs have been regarded as keystone plant resources that support diverse tropical vertebrate frugivore communities. Planting or conserving large fig trees, such as stranglers, has therefore been proposed for enhancing urban biodiversity. We compared the diversity and community structure of bird assemblages on strangler figs with non-fig urban trees as well as between the fruiting and non-fruiting fig trees in an urban setting in Singapore. The total bird abundance across all the fig trees when in fruit was 4.5-fold higher than on non-fig trees and 3.5-fold higher than when the same fig trees were not fruiting, but only attracted two more species. On individual trees, after accounting for the presence of mistletoes, tree height, the area covered by buildings and road lane density, and distance to natural vegetation, mean diversity was not different between non-fig trees and fig trees when they were not in fruit. On the other hand, when fruiting, each fig tree on average had 1.4 more species, 3 more counts of non-native birds, and 1.6 more counts of insectivorous birds than when not fruiting. There was significant compositional turnover between non-fig trees and non-fruiting fig trees, while community dispersion was significantly lower among fig trees in fruit. Our results demonstrate that fig trees provide fruit and non-fruit resources for birds in an urban landscape but do not necessarily support a more diverse total bird assemblages than non-fig trees. Instead, bird communities on fruiting urban figs would be highly homogeneous and dominated by a few species.
Data from: Functional richness shows spatial scale dependency in Pheidole ant assemblages from Neotropical savannas
There is a growing recognition that spatial scale is important for understanding ecological processes shaping community membership, but empirical evidence on this topic is still scarce. Ecological processes such as environmental filtering can decrease functional differences among species and promote functional clustering of species assemblages, whereas interspecific competition can do the opposite. These different ecological processes are expected to take place at different spatial scales, with competition being more likely at finer scales and environmental filtering most likely at coarser scales. We used a comprehensive dataset on species assemblages of a dominant ant genus, Pheidole, in the Cerrado (savanna) biodiversity hotspot to ask how functional richness relate to species richness gradients and whether such relationships vary across spatial scales. Functional richness of Pheidole assemblages decreased with increasing species richness, but such relationship did not vary across different spatial scales. Species were more functionally dissimilar at finer spatial scales, and functional richness increased less than expected with increasing species richness. Our results indicate a tighter packing of the functional volume as richness increases and point out to a primary role for environmental filtering in shaping membership of Pheidole assemblages in Neotropical savannas.
Which pitfall traps and sampling effort to choose to evaluate cropping system effects on spider and carabid assemblages?
<p>Dataset and example of the script (R) used in the simulation approach.</p>
Dominance of endemics in the reef fish assemblages of the Hawaiian Archipelago
<p>Aim: Species ranges provide a valuable foundation for resolving biogeographic regions, evolutionary processes, and extinction risks. To inform conservation priorities, here we develop the first bioregionalization based on reef fish abundance of the Hawaiian Archipelago, which spans nearly 10° of latitude across 2,400 km, including 8 high volcanic islands in the populated main Hawaiian Islands (MHI), and 10 low islands (atolls, shoals, and islets) in the remote northwestern Hawaiian Islands (NWHI)..</p> <p>Location: The Hawaiian Archipelago.</p> <p>Taxon: Fishes (276 taxa).</p> <p>Methods: We compiled 5,316 visual fish surveys at depths of 1-30 m from throughout the Hawaiian Archipelago. Geographic range (km2) for each species was measured as extent of occurrence (EOO) and area of occurrence (AOO). PERMANOVA and PCO were used to investigate drivers of fish assemblage structure. Distance-based multivariate analyses were used to evaluate the relationship between fish assemblage structure and predictor variables including latitude, reef area, temperature, chlorophyll-a, wave-energy, and human population density.</p> <p>Results: Distinct fish assemblages exist in the MHI and NWHI, with two additional faunal breaks driven primarily by endemic species abundance. Latitude explained 37% of the variability in fish assemblages, with reef area accounting for an additional 9%. EOO showed a significant correlation with latitude. Endemics comprised 52-55% of the numerical abundance at the northern end of the archipelago but only 17% on Hawai'i Island in the extreme south. Maximum size and activity regime (day vs. night) explained the most variation in the abundance of endemics.</p> <p>Main conclusions: The Hawaiian fish assemblages are strongly influenced by endemic species, affirming the archipelago as a biodiversity hotspot of high conservation value. The higher abundance of endemics in the NWHI may represent preadaptation to oceanic (oligotrophic) conditions. Resolution of distinct bioregions across the archipelago provides a better understanding of reef fish macroecology, with implications for management at the archipelago scale.</p>
Multiscale drivers of carabid beetle (Coleoptera: Carabidae) assemblages in small European woodlands
<p><strong>Aim </strong>The spatiotemporal connectivity of forest patches in lowland agricultural landscapes and their age matter to explain current biodiversity patterns across regional as well as biogeographical extents, to the point that it exceeds the contribution of macroclimate for plant diversity in the understory of temperate forests. Whether this holds true for other taxonomic groups remains largely unknown. Yet, it has important consequences for ecosystem functioning and the delivery of ecosystem services. Focusing on carabid beetle assemblages, we assessed the relative importance of macroclimatic, landscape, and patch attributes on driving local species richness (-diversity) and species dissimilarity between patches (-diversity).</p> <p><strong>Location</strong> Deciduous forest patches in seven regions along a 2,100-km long latitudinal gradient across the European temperate forest biome, from southern France to central Sweden.</p> <p><strong>Methods</strong> We sampled 221 forest patches in two 55-km landscape windows with contrasting management intensities. Carabid beetles were classified into four habitat-preference guilds: forest-specialist, forest-generalist, eurytopic, and open-habitat species. We quantified the multi-level environmental influence using mixed-effects models and variation partitioning analysis.</p> <p><strong>Results</strong> We found that both - and -diversity were primarily determined by macroclimate, acting as a large-scale ecological filter on carabid assemblages among regions. Forest-patch conditions, including biotic and abiotic heterogeneity as well as patch age (but not patch size), increased -diversity of forest species. Landscape management intensity weakly influenced -diversity of forest species, but increased the number of non-forest species in forest patches. Beta-diversity of non-forest species increased with patch heterogeneity and decreased with landscape management intensity.</p> <p><strong>Main conclusions</strong> Our results highlight the leading role of broad macroclimatic gradients over local and landscape factors in determining the composition of local carabid communities, thereby shedding light on macroecological patterns of arthropod assemblages. This study emphasizes the urgent need for preserving ancient forest patches embedded in agricultural landscapes, even the small and weakly connected ones.</p>
Data from: Modern pollen assemblages of the Neotropics
<p><strong>Aim:</strong> To provide a database of modern pollen abundances from a diversity of Neotropical locations.</p> <p><strong>Location:</strong> The Neotropics, especially western Amazonia, the Andes, The Galápagos, Central America, Puerto Rico, and Mexico.</p> <p><strong>Methods:</strong> Over a 30-year period, mud-water interface samples, moss polsters, soils, and pollen traps were used to assay modern pollen rain. Standard extraction methods were used and a minimum of 300 terrestrial pollen grains counted and identified per sample. Bioclimatic data were assigned to each location, and sexual traits and pollination syndromes are provided for some genera. A detrended correspondence analysis (DCA) shows the structuring of the data relative to mean annual temperatures (MAT), mean annual precipitation (MAP), and precipitation of the driest quarter (PDQ). Probability density functions of distances among samples are calculated within and between Holdridge Life Zones, based on sample DCA scores.</p> <p><strong>Results:</strong> The modern pollen of 636 locations are documented, with >500 pollen types identified. The dataset spans settings with MAT < 5oC to >25oC, and with MAP ranging from c. 500-5000 mm, and PDQ from 80 - 1500 mm. Ordination of the dataset provides evidence that assemblages differ according to temperature and precipitation, although historical biogeography also shapes pollen rains. The pollen grains of zoophilous species contribute important information to habitat descriptions, but they are under-represented in the dataset.</p> <p><strong>Main conclusions:</strong> The dataset covers a broad environmental range and can help inform biogeographic and paleoenvironmental interpretation of paleoecological records. Some caution in using the data is needed as the field of tropical palynology is maturing and the data gathered 30 years ago are less detailed than those gathered recently. Although anemophilous taxa tend to be over-represented in neotropical pollen spectra, the majority of pollen identified in each sample are from zoophilous species.</p>
FIG. 2. — Profil taphonomique des principaux assemblages fauniques d in Exploitation animale à l'Ancien Empire en Égypte: les apports d'Ayn Asil (oasis de Dakhla)
FIG. 2. — Profil taphonomique des principaux assemblages fauniques d'Ayn Asil.
Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: lessons from natural assemblages
<p>1. Functional diversity assessments are crucial and increasingly used for understanding ecological processes and managing ecosystems. The functional diversity of a community is assessed by sampling traits at one or more scales (individuals, populations, species) and calculating a summary index of the variation in trait values. However, it remains unclear how the scale at which traits are sampled and the indices used to estimate functional diversity may alter the patterns observed and inferences about ecological processes.</p> <p>2. For 40 plant and 61 ant communities, we assess functional diversity using six methods – encompassing various mean-based and probabilistic methods – chosen to reflect common scenarios where different levels of detail are available in trait data. We test whether including trait variability at different scales (from individuals to species) alter functional diversity values calculated using volume-based and dissimilarity-based indices, Functional Richness (FRic) and Rao, respectively. We further test whether such effects alter the functional diversity patterns observed across communities and their relationships with environmental drivers such as abiotic gradients and occurrences of invasive species.</p> <p>3. Intraspecific trait variability strongly determined FRic and Rao. Methods using only species' mean trait values to calculate FRic (convex hulls) and Rao (Gower-based dissimilarity) distorted the patterns observed when intraspecific trait variability was considered. These distortions generated Type I and Type II errors for the effects of environmental factors structuring the plant and ant communities.</p> <p>4. The high sensitivity of FRic to individuals with extreme trait values was revealed in comparisons of different probabilistic methods including among-individual and among-population trait variability in functional diversity. By contrast, values and ecological patterns in Rao were consistent among methods including different scales of intraspecific trait variability.</p> <p>5. Decisions about where traits are sampled and how trait variability is included in functional diversity can drastically change the patterns observed and conclusions about ecological processes. We recommend sampling the traits of multiple individuals per species and capturing their intraspecific trait variability using probabilistic methods. We discuss how intraspecific trait variability can be reasonably estimated and included in functional diversity in the common circumstance where only limited trait data are available.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.